In my version (and this may be controversial) the clones don't form an army at all. The Clone referred to in the name "The Clone Wars" is just one person - the leader of the antagonistic army. It is discovered in Episode II that he is a genetic reproduction of an extinct race of warriors.
I've decided to do this for a number of reasons. Firstly, the idea of the Galactic Republic - i.e, the good guys - using an army of mindless soldiers bred only to fight and die seemed a little morally warped to me. The Kaminoans even mention them being bred for perfect obedience.
This just doesn't stike me as something that the moral old Obi-Wan or the spiritual Yoda would have anything to do with. Yoda and Obi-Wan seem to me to be the type to emphasise the importance of the liberty of all sentient beings, and a clone army runs entirely contrary to such concepts.
So, what would later be dubbed "The Clone Wars" are already in full swing by the time Episode I opens - it's just not yet being called "The Clone Wars". Rather like the Galactic Civil War of the original trilogy, the Clone Wars would be the war of this Star Wars trilogy.
Interesting. I agree with you about the good guys having clones, I was surprised that the moral implications of slave soldiers wasn't even addressed. I thought it a bit odd that the Jedi were totally on board for that one. What I've done is have the clones as the "bad guys" as well. But it's a clone army, not just one man. I think it was always intended to be that way, wars are named after the enemy if they only mention one side, logical, otherwise you'd just have to number them all -- the Barbary Wars would be like American War V. Or like calling the French and Indian War, the British and American War, just stupid.
Suggestions would be appreciated here.
Since you asked for suggestions, what I've done is just have Anakin allude to it. Anakin and Owen were refugees from a planet that the clones attacked in my story and they ended up fleeing to Tatooine. Owen chose to stay there and make a new life, but Anakin chose to get involved although Owen tried to convince him not to, believing they should just cut their losses and that Tatooine is far enough removed from the conflict and that they wouldn't have to worry about any more trouble if they settled out in the middle of nowhere. (Of course Owen ends up being totally wrong.) I have it happen in the past from where I start my story. You don't need to have it on screen, you can just have Anakin talk about it to another character like I did. I don't think it's worth a scene unless Owen is a major character in your story, just a suggestion. =)